Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-18 Thread Mark Abraham 
Hi,

You're not compiling properly for your cluster, which might have different
hardware in different places. Read its docs and talk to your admins.

Mark

On Mon, Sep 18, 2017 at 4:07 AM Vidya R  wrote:

> Thank you for your reply.
>
> When I try to run my job in a single processor through qsub command, (by
> feeding the gromacs mdrun command in script file), it says SEGMENTATION
> FAULT, CORE DUMPED...
>
>
> But, when I run my job in login node (which we are not supposed to do), it
> works very well...
>
>
> Can you comment on this?
>
>
> Thanks,
> Vidya.R
>
> On Mon, Sep 18, 2017 at 2:50 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You're running a thread-MPI version of GROMACS, which is probably not
> what
> > you want to do if you're running mpirun. It should work even so, but
> > whatever quirks exist with SGE are unfortunately between you, its docs
> and
> > your cluster's docs and admins :-(
> >
> > Mark
> >
> > On Sun, Sep 17, 2017 at 7:23 AM Vidya R  wrote:
> >
> > > My log file is provided in the link below
> > >
> > > Can you please look into it and let me know why the error arises?
> > >
> > > I am feeding my commands in SGE cluster.   When I run it in my login
> > node,
> > > gmx mdrun -v -deffnm eql runs well
> > >
> > >
> > > But, through qsub command, (with 8 processors) It says,
> > >
> > > mpirun noticed that process rank 7 with PID 19160 on node
> > > compute-0-28.local exited on signal 11 (Segmentation fault).
> > >
> > > Please help me.
> > >
> > > I am unable to figure out, as to whether the problem is with the
> version
> > of
> > > gromacs or the method of compiling.
> > >
> > >
> > >
> > > https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/
> > view?usp=sharing
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-17 Thread Vidya R 
Thank you for your reply.

When I try to run my job in a single processor through qsub command, (by
feeding the gromacs mdrun command in script file), it says SEGMENTATION
FAULT, CORE DUMPED...


But, when I run my job in login node (which we are not supposed to do), it
works very well...


Can you comment on this?


Thanks,
Vidya.R

On Mon, Sep 18, 2017 at 2:50 AM, Mark Abraham 
wrote:

> Hi,
>
> You're running a thread-MPI version of GROMACS, which is probably not what
> you want to do if you're running mpirun. It should work even so, but
> whatever quirks exist with SGE are unfortunately between you, its docs and
> your cluster's docs and admins :-(
>
> Mark
>
> On Sun, Sep 17, 2017 at 7:23 AM Vidya R  wrote:
>
> > My log file is provided in the link below
> >
> > Can you please look into it and let me know why the error arises?
> >
> > I am feeding my commands in SGE cluster.   When I run it in my login
> node,
> > gmx mdrun -v -deffnm eql runs well
> >
> >
> > But, through qsub command, (with 8 processors) It says,
> >
> > mpirun noticed that process rank 7 with PID 19160 on node
> > compute-0-28.local exited on signal 11 (Segmentation fault).
> >
> > Please help me.
> >
> > I am unable to figure out, as to whether the problem is with the version
> of
> > gromacs or the method of compiling.
> >
> >
> >
> > https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/
> view?usp=sharing
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-17 Thread Mark Abraham 
Hi,

You're running a thread-MPI version of GROMACS, which is probably not what
you want to do if you're running mpirun. It should work even so, but
whatever quirks exist with SGE are unfortunately between you, its docs and
your cluster's docs and admins :-(

Mark

On Sun, Sep 17, 2017 at 7:23 AM Vidya R  wrote:

> My log file is provided in the link below
>
> Can you please look into it and let me know why the error arises?
>
> I am feeding my commands in SGE cluster.   When I run it in my login node,
> gmx mdrun -v -deffnm eql runs well
>
>
> But, through qsub command, (with 8 processors) It says,
>
> mpirun noticed that process rank 7 with PID 19160 on node
> compute-0-28.local exited on signal 11 (Segmentation fault).
>
> Please help me.
>
> I am unable to figure out, as to whether the problem is with the version of
> gromacs or the method of compiling.
>
>
>
> https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/view?usp=sharing
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-17 Thread Vidya R 
https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU
/view?usp=sharing=59be86ad

On Sun, Sep 17, 2017 at 6:35 PM, Justin Lemkul  wrote:

>
>
> On 9/17/17 1:22 AM, Vidya R wrote:
>
>> My log file is provided in the link below
>>
>> Can you please look into it and let me know why the error arises?
>>
>> I am feeding my commands in SGE cluster.   When I run it in my login node,
>> gmx mdrun -v -deffnm eql runs well
>>
>>
>> But, through qsub command, (with 8 processors) It says,
>>
>> mpirun noticed that process rank 7 with PID 19160 on node
>> compute-0-28.local exited on signal 11 (Segmentation fault).
>>
>> Please help me.
>>
>> I am unable to figure out, as to whether the problem is with the version
>> of
>> gromacs or the method of compiling.
>>
>>
>> https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU
>> /view?usp=sharing
>>
>>
> I am unable to view the file, as it says I do not have permission.  Please
> change the access restrictions on it.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
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Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-17 Thread Justin Lemkul 



On 9/17/17 1:22 AM, Vidya R wrote:

My log file is provided in the link below

Can you please look into it and let me know why the error arises?

I am feeding my commands in SGE cluster.   When I run it in my login node,
gmx mdrun -v -deffnm eql runs well


But, through qsub command, (with 8 processors) It says,

mpirun noticed that process rank 7 with PID 19160 on node
compute-0-28.local exited on signal 11 (Segmentation fault).

Please help me.

I am unable to figure out, as to whether the problem is with the version of
gromacs or the method of compiling.


https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/view?usp=sharing



I am unable to view the file, as it says I do not have permission.  Please 
change the access restrictions on it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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[gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

2017-09-16 Thread Vidya R 
My log file is provided in the link below

Can you please look into it and let me know why the error arises?

I am feeding my commands in SGE cluster.   When I run it in my login node,
gmx mdrun -v -deffnm eql runs well


But, through qsub command, (with 8 processors) It says,

mpirun noticed that process rank 7 with PID 19160 on node
compute-0-28.local exited on signal 11 (Segmentation fault).

Please help me.

I am unable to figure out, as to whether the problem is with the version of
gromacs or the method of compiling.


https://drive.google.com/file/d/0BxGqxeGwTDLbQW9OZDFuM1doUlU/view?usp=sharing
-- 
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